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How to filter the BAM file using barcode list produced by 10x pipelines?

Hi everyone,

I have a barcode list I want to filter that barcode from my bam file using the below-mentioned tutorial.

https://kb.10xgenomics.com/hc/en-us/articles/360022448251-How-to-filter-the-BAM-file-produced-by-10x-pipelines-with-a-list-of-barcodes-

But if I use CB:Z: tag, as mentioned in the tutorial with barcode i.e. filter.txt file it doesn't work I can't able to generate "filtered_SAM_body" it, seems like 0 bytes.

Any Suggestions will be highly appreciated.

Thank you.

list barcode
• 1,667 views • link
updated by GenoMax GenoMax • written by Info.shi • Info.shi

1 answer

Hey,

Information is a bit late but incase you still need to know you can use the -d flag from older versions of samtools like v1.17.

samtools view -D CB:filter.txt file.bam -h -b -o new.bam
• 0 views • link
updated by GenoMax GenoMax • written by ashwini • ashwini

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